Delete operation history from python?
I believe the answer is no.
However, you can clear the list by saving and reopening the .blend:
From the UI:

Save the file with CtrlS

Reload it with CtrlShiftO1


With python:

Save the file with save_mainfile()

Open the file with open_mainfile()


For example:
import bpy

file=&quot;/tmp/test.blend&quot;
bpy.ops.wm.save_mainfile(filepath=file)
bpy.ops.wm.open_mainfile(filepath=file)